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Publications

2023

Dimensionality Engineering of Lead Organic Chalcogenide Semiconductors

H Yang, S Mandal, YH Lee, JY Park, H Zhao, C Yuan, L Huang, M Chen, Letian Dou, Journal of the American Chemical Society

Backdiff: a Diffusion Model for Generalized Transferable Protein Backmapping

Y Liu, M Chen, G Lin, arXiv preprint arXiv:2310.01768

Molecular van der Waals Fluids in Cavity Quantum Electrodynamics

JP Philbin, TS Haugland, TK Ghosh, E Ronca, M Chen, P Narang, H Koch, The Journal of Physical Chemistry Letters 14 (40), 8988-8993

Factors Controlling Intercalation of Metal Atoms into WS2: Implications for Electronically Tunable Semiconductors

K Zhu, Y Tao, S Mandal, M Chen, CW Li, ACS Applied Nano Materials

Understanding the polaritonic ground state in cavity quantum electrodynamics

TS Haugland, JP Philbin, TK Ghosh, M Chen, H Koch, P Narang, arXiv:2307.14822

Manifold Learning in Atomistic Simulations: A Conceptual Review

J. Rydzewski, M. Chen, O. Valsson,  arXiv:2303.08486

Structure Optimization with Stochastic Density Functional Theory. 

M. Chen, R. Baer, E. Rabani, arXiv preprint, The Journal of Chemical Physics 158 (2)

2022

Reweighted Manifold Learning of Collective Variables from Enhanced Sampling Simulations

J Rydzewski, M Chen, TK Ghosh, O Valsson, Journal of Chemical Theory and Computation 18 (12), 7179-7192

Molecular van der Waals fluids in cavity quantum electrodynamics

JP Philbin, TS Haugland, TK Ghosh, E Ronca, M Chen, P Narang, H Koch, arXiv preprint arXiv:2209.07956

Constraining elemental partitioning and isotope fractionation of mantle minerals with in-situ single crystal X-ray diffraction

D. Zhang, J. Xu, P. Dera, B. Chen, M. Chen, P. Eng, V. Prakapenka, 2022 Goldschmidt Conference

2021

Silicon isotope fractionation constrained by single crystal X-ray diffraction

D. Zhang, M. Chen, P. Dera, P. Eng, AGU Fall Meeting Abstracts, MR12A-05

Collective variable-based enhanced sampling and machine learning

M. Chen, The European Physical Journal B 94, 211

Experimental calibration of the reduced partition function ratios of tetrahedrally coordinated silicon from the Debye–Waller factors

D. Zhang, M. Chen, P. Dera, P. Eng, Contributions to Mineralogy and Petrology 176 (9), 1-17

Stochastic density functional theory: Real-and energy-space fragmentation for noise reduction

M. Chen, R. Baer, D. Neuhauser, E. Rabani, The Journal of Chemical Physics 154 (20), 204108

Boost Efficiency for Stochastic Density Functional Theory with a Unified Strategy

M Chen, R Baer, D Neuhauser, E Rabani, APS March Meeting Abstracts 2021, F19. 008

2020

Range-separated stochastic resolution of identity: Formulation and application to second-order Green’s function theory

W. Dou, M. Chen, T.Y. Takeshita, R. Baer, D. Neuhauser, E. Rabani, The Journal of chemical physics 153 (7), 074113

Dopant levels in large nanocrystals using stochastic optimally tuned range-separated hybrid density functional theory

A.J. Lee, M. Chen, W. Li, D. Neuhauser, R. Baer, E. Rabani, Physical Review B 102 (3), 035112

Stochastic resolution of identity to second order Green’s function: ground-state and quasi-particle properties.

W. Dou, T. Takeshita, M. Chen, R. Baer, D. Neuhauser, E. Rabani, Bulletin of the American Physical Society 65

2019

Stochastic embedding DFT: Theory and application to p-nitroaniline in water

W. Li, M. Chen, E. Rabani, R. Baer, D. Neuhauser, The Journal of chemical physics 151 (17), 174115

Stochastic Resolution of Identity for Real-Time Second-Order Green’s Function: Ionization Potential and Quasi-Particle Spectrum

W. Dou, T.Y. Takeshita, M. Chen, R. Baer, D. Neuhauser, E. Rabani, Journal of chemical theory and computation 15 (12), 6703-6711

Energy window stochastic density functional theory

M. Chen, R. Baer, D. Neuhauser, E. Rabani, The Journal of chemical physics 151 (11), 114116

Stochastic embedding DFT: theory and application to p-nitroaniline

W. Li, M. Chen, E. Rabani, R. Baer, D. Neuhauser, arXiv preprint arXiv:1905.07099

Overlapped embedded fragment stochastic density functional theory

M. Chen, D. Neuhauser, R. Baer, E. Rabani, ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 257

Overlapped embedded fragment stochastic density functional theory for covalently-bonded materials

M. Chen, R. Baer, D. Neuhauser, E. Rabani, The Journal of chemical physics 150 (3), 034106

Shieldnets: Defending against adversarial attacks using probabilistic adversarial robustness

R. Theagarajan, M. Chen, B. Bhanu, J. Zhang, Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition

2018

Unfolding hidden barriers by active enhanced sampling

J. Zhang, M. Chen, Physical review letters 121 (1), 010601

2016

Resorcinol crystallization from the melt: a new ambient phase and new “riddles”

Q. Zhu, A.G. Shtukenberg, D.J. Carter, T.Q. Yu, J. Yang, M. Chen, P. Raiteri, et al., Journal of the American Chemical Society 138 (14), 4881-4889

Exploring and Sampling on High Dimensional Free Energy Surfaces

​M. Chen, New York University

2015

Locating landmarks on high-dimensional free energy surfaces

M Chen, TQ Yu, ME Tuckerman, Proceedings of the National Academy of Sciences 112 (11), 3235-3240

2014

Order-parameter-aided temperature-accelerated sampling for the exploration of crystal polymorphism and solid-liquid phase transitions

T.Q. Yu, P.Y. Chen, M. Chen, A. Samanta, E. Vanden-Eijnden, M. Tuckerman, The Journal of chemical physics 140 (21), 06B603_1

Sampling saddle points on a free energy surface

A. Samanta, M. Chen, T.Q. Yu, M. Tuckerman, W E, The Journal of Chemical Physics 140 (16), 04B610_1

2012

Exploring the free energy landscapes of biomolecules and crystalline polymorphs

M.E. Chen, T.Q.E. Yu, M.E. Cuendet, M.E. Tuckerman, ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 244

Heating and flooding: A unified approach for rapid generation of free energy surfaces

M. Chen, M.A. Cuendet, M.E. Tuckerman, The Journal of Chemical Physics 137 (2), 024102

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